scholarly journals Supersized ribosomal RNA expansion segments in Asgard archaea

2019 ◽  
Author(s):  
Petar I. Penev ◽  
Sara Fakhretaha-Aval ◽  
Vaishnavi J. Patel ◽  
Jamie J. Cannone ◽  
Robin R. Gutell ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Ribosomal Rna ◽  
Common Core ◽  
Ribosomal Proteins ◽  
Common Ancestor ◽  
Large Subunit ◽  
Cell Lineages ◽  
Accretion Model ◽  
The Common ◽  
Lsu Rrna

The ribosome's common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is most similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNA. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from the presence of two supersized ESs, ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. While Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.

scholarly journals Supersized Ribosomal RNA Expansion Segments in Asgard Archaea

2020 ◽  
Vol 12 (10) ◽  
pp. 1694-1710
Author(s):  
Petar I Penev ◽  
Sara Fakhretaha-Aval ◽  
Vaishnavi J Patel ◽  
Jamie J Cannone ◽  
Robin R Gutell ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Ribosomal Rna ◽  
Common Core ◽  
Ribosomal Proteins ◽  
Common Ancestor ◽  
Ribosomal Subunit ◽  
Large Ribosomal Subunit ◽  
Cell Lineages ◽  
Accretion Model ◽  
The Common

Abstract The ribosome’s common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large ribosomal subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from two supersized ESs, called ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. Although Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.

Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3115-3123 ◽  
Author(s):  
Neža Čadež ◽  
Dénes Dlauchy ◽  
Peter Raspor ◽  
Gábor Péter
Keyword(s):  
Sequence Analysis ◽  
Olive Oil ◽  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Virgin Olive Oil ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Lsu Rrna

Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322T = CBS 12778T = NRRL Y-63657T), Ogataea histrianica sp. nov. (type strain: ZIM 2463T = CBS 12779T = NRRL Y-63658T) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896T = CBS 12735T = NRRL Y-63656T).

scholarly journals Modular assembly of the nucleolar large subunit processome

2017 ◽  
Author(s):  
Zahra Assur Sanghai ◽  
Linamarie Miller ◽  
Kelly R. Molloy ◽  
Jonas Barandun ◽  
Mirjam Hunziker ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Molecular Mimicry ◽  
Large Subunit ◽  
Ribosome Assembly ◽  
Modular Assembly ◽  
Assembly Result ◽  
Concerted Activity ◽  
Folding Pathways ◽  
Exit Tunnel

Early co-transcriptional events of eukaryotic ribosome assembly result in the formation of the small and large subunit processomes. We have determined cryo-EM reconstructions of the nucleolar large subunit processome in different conformational states at resolutions up to 3.4 Ångstroms. These structures reveal how steric hindrance and molecular mimicry are used to prevent premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Mutually exclusive conformations of these particles suggest that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly.

scholarly journals Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis and its link to the common house gecko (Hemidactylus frenatus) as a potential risk factor

2018 ◽  
Author(s):  
Ali Al Bshabshe ◽  
Martin R.P. Joseph ◽  
Ahmed M. Al Hakami ◽  
Tarig Al Azraqi ◽  
Sulieman Al Humayed ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Ribosomal Rna ◽  
Large Subunit ◽  
Causal Agent ◽  
Gut Contents ◽  
Ribosomal Rna Gene ◽  
Source Of Infection ◽  
The Common ◽  
Hemidactylus Frenatus ◽  
Common House

ABSTRACTBasidiobolus spp. are a significant causal agent of infections in man and animals including gastrointestinal basidiobolomycosis (GIB). Little information is available on how these infections are acquired or transmitted, apart from the postulation that environmental sources are implicated. This study aimed to identify Basidiobolus spp. from GIB patients and from the house gecko as a possible source of infection in Aseer, Saudi Arabia. Basidiobolus spp. were isolated from patient specimens (colonic mass biopsy) and from house gecko (gut contents) from Muhayil Aseer areas, in southern Saudi Arabia, using Sabouraud dextrose agar (SDA) which was incubated aerobically for up to three weeks at 30°C. Isolated fungi were initially identified using classical mycological tools and confirmed by sequence analysis of the large subunit ribosomal RNA gene. Cultured specimens from humans and geckos revealed phenotypically similar zygomycete-like fungi which conform to those of Basidiobolus species. The strains formed a monophyletic clade in the 28S ribosomal RNA gene phylogenetic tree. They shared 99.97% similarity with B. haptosporus and 99.97% with B. haptosporus var. minor but have a relatively remote similarity to B. ranarum (99.925%). One isolates from a gecko (L3) fall within the sub-clade encompassing B. haptosporus strain NRRL28635. The study strongly suggests a new and a serious causal agent of GIB related to Basidiobolus haptosporus. The isolation of identical Basidiobolus haptosporus-like strains from humans and lizards from one area is an important step towards identifying risk factors for GIB. Research is underway to screen more environmental niches and fully describe the Basidiobolus strains.

scholarly journals The 23S Ribosomal RNA From Pyrococcus furiosus Is Circularly Permuted

2020 ◽  
Vol 11 ◽  
Author(s):  
Ulf Birkedal ◽  
Bertrand Beckert ◽  
Daniel N. Wilson ◽  
Henrik Nielsen
Keyword(s):  
Ribosomal Rna ◽  
Pyrococcus Furiosus ◽  
Large Subunit ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Interaction Site ◽  
Cellular Processes ◽  
Lsu Rrna ◽  
23S Ribosomal Rna ◽  
Primary Interaction

Synthesis and assembly of ribosomal components are fundamental cellular processes and generally well-conserved within the main groups of organisms. Yet, provocative variations to the general schemes exist. We have discovered an unusual processing pathway of pre-rRNA in extreme thermophilic archaea exemplified by Pyrococcus furiosus. The large subunit (LSU) rRNA is produced as a circularly permuted form through circularization followed by excision of Helix 98. As a consequence, the terminal domain VII that comprise the binding site for the signal recognition particle is appended to the 5´ end of the LSU rRNA that instead terminates in Domain VI carrying the Sarcin-Ricin Loop, the primary interaction site with the translational GTPases. To our knowledge, this is the first example of a true post-transcriptional circular permutation of a main functional molecule and the first example of rRNA fragmentation in archaea.

Rapid evolution in sequence and length of the nuclear-located gene for mitochondrial L2 ribosomal protein in cereals

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 275-281 ◽  
Author(s):  
Selvi Subramanian ◽  
Linda Bonen
Keyword(s):  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Large Subunit ◽  
Rapid Evolution ◽  
Comparative Sequence Analysis ◽  
Marchantia Polymorpha ◽  
Peptidyl Transferase

The L2 ribosomal protein is typically one of the most conserved proteins in the ribosome and is universally present in bacterial, archaeal, and eukaryotic cytosolic and organellar ribosomes. It is usually 260–270 amino acids long and its binding to the large-subunit ribosomal RNA near the peptidyl transferase center is mediated by a β-barrel RNA-binding domain with 10 β strands. In the diverse land plants Marchantia polymorpha (liverwort) and Oryza sativa (rice), the mitochondrial-encoded L2 ribosomal protein is about 500 amino acids long owing to a centrally located expansion containing the β3–β4 strand region. We have determined that, in wheat, the functional rpl2 gene has been trans ferred to the nucleus and much of the plant-specific internal insert has been deleted. Its mRNA is only 1.2 kb, and two expressed copies in wheat encode proteins of 318 and 319 amino acids, so they are considerably shorter than the maize nuclear-located rpl2 gene of 448 codons. Comparative sequence analysis of cereal mitochondrial L2 ribosomal proteins indicates that the mid region has undergone unexpectedly rapid evolution during the last 60 million years.Key words: mitochondria, ribosomal protein, plants, evolutionary gene transfer.

scholarly journals Simplification of Ribosomes in Bacteria with Tiny Genomes

2020 ◽  
Vol 38 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Daria D Nikolaeva ◽  
Mikhail S Gelfand ◽  
Sofya K Garushyants
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Protein Biosynthesis ◽  
Large Subunit ◽  
Protein Composition ◽  
Small Subunit ◽  
Bacterial Genomes ◽  
Shine Dalgarno Sequence

Abstract The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine–Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.

scholarly journals Single-stranded DNA-binding proteins (SSBs) -- sources and applications in molecular biology.

2005 ◽  
Vol 52 (3) ◽  
pp. 569-574 ◽  
Author(s):  
Józef Kur ◽  
Marcin Olszewski ◽  
Anna Długołecka ◽  
Paweł Filipkowski
Keyword(s):  
Dna Binding ◽  
Molecular Biology ◽  
Common Core ◽  
Binding Proteins ◽  
Common Ancestor ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Single Stranded Dna ◽  
Ssdna Binding ◽  
The Common

Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria, archaea and eukarya. The SSBs share a common core ssDNA-binding domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. In recent years, there has been an increasing interest in SSBs because they are useful for molecular biology methods and for analytical purposes. In this review, we concentrate on recent advances in the discovery of new sources of SSBs as well as certain aspects of their applications in analytical sciences.

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